When PCem is updated do I have to reinstall all my Windows and DOS systems or there is no problem with version change?

Usually you can keep everything but it's a good idea to create a backup of your previous PCem folder and your floppy/zip/hard disc images if those are on another folder before trying a new version, this way if something goes incompatible or buggy you won't lose your job until the problem gets fixed.

Making regular backups is very useful also if a machine hangs and the disc image gets corrupted, you have problems due to intallation of new programs or drivers on the emulated machines and so on.

To make backups remember to close PCem first, even the Configuration Manager window, otherwise you can end with an incomplete or corrupted backup.

Also not sure if it's real behavior or not anymore as it's been so long, Silpheed on IBM XT 4.77mhz has some serious keyboard control issues the faster machines don't have. Arrow keys stick or don't respond. 8088/4.77, 512kb RAM, CGA

I've played Commandos BEL and BCD for a few minutes with S3 Trio64 with 1MB and it's fine too with full versions of those games,
but only after reinstalling DirectX to update video drivers and setting desktop color depth to 16 bit, in 256 colors it refuses to start, says can't find DirectX 5

Maybe should you add in the "Not bug" category "Pictionary " and "Hitman: Codename 47" (this later game has crashes with Glide, but works fine with Direct3D)
I made a review here: viewtopic.php?f=3&t=640

Buggy:
- Age of Empires II (Hangs in 1024x768. 800x600 fine. In-game window issues (i.e. opening the chat window will have the top half of the screen stuck without updates))
- Darkened Skye (crashes PCem when you access one of the menus)

I guess that "flushing" all keys pressed (so the keyboard status is without any key pressed) after recovering focus will do the trick. Or maybe is a flag (like "Ctrl was pressed")? In any case, pressing again Ctrl to "unstuck" the keyboard does not work.

Ok so I went hunting around the internet [Moderator edit - link removed]

Take note of [], this seems to be an Image of an official cumulative update disk released by Microsoft in 2004, and on it is every official update for Windows 98 and Windows ME, including the non security fixes. If you are wanting a way to install all the official fixes for win9x without the unofficial bluescreen inducing frankenbuild crap, then this is what you are looking for.

The other ISO's have updates for WIndows95 but they are a loose collection.

Anyway, after running the installer contained on [] within Windows 98 SE, Croc now works! I wonder what else having these fixes?

I thought that would have been allowed as it is purely a iso image containing updates once freely downloadable by anyone from the windows update website before they got removed after support was dropped. It's not the whole OS.